DESCRIPTION: Although smoking and alcohol use are major risk factors for squamous cell carcinoma of the head and neck (SCCHN), only a fraction of smokers develops SCCHN, suggesting a role for genetic susceptibility. We have found an association between increasing risk of SCCHN and suboptimal DNA repair capacity (DRC) that may be determined by adverse genetic variants such as single nucleotide polymorphisms (SNPs) in the nucleotide-excision repair (NER) genes. Therefore, we propose to focus in depth on the NER pathway by expanding from previously studied 5 non-synonymous SNPs (nsSNPs) to 85 common tagging SNPs (tSNPs) in the well-defined 8 core NER genes (i.e., ERCC1, XPA, XPB, XPC, XPD, XPE, XPF, and XPG), to correlate the variant alleles/genotypes or haplotypes/diplotypes with three NER phenotypes (i.e., NER mRNA expression, NER protein expression and NER DRC), and to evaluate their associations with risk of SCCHN. To accomplish these goals, we will include 1,600 SCCHN cases and 1,600 age-, sex-, and ethnicity-matched controls that consist of previously recruited 800 cases and 800 controls and an additional 800 cases and 800 controls to be recruited in this application using the same study design, selection criteria, and data collection instruments. To perform a comprehensive analysis of NER in SCCHN, our specific aims are: AIM 1: To determine the associations of the frequencies of variant alleles/haplotypes and genotypes/diplotypes of tSNPs in the 8 NER genes and the DRC phenotype with risk of SCCHN in 1,600 SCCHN cases and 1,600 controls. We will test the hypotheses that adverse alleles/haplotypes or genotypes/diplotypes of these selected genes and suboptimal DRC phenotype are associated with increased risk of SCCHN. AIM 2: To determine mRNA and protein expression levels of the 8 NER proteins by real-time RT-PCT assay and high-throughput reverse-phase protein lysate microarray assay, respectively, in cultured lymphocytes from 400 cases and 400 controls to be accrued. We will test the hypothesis that lower levels of NER mRNA and protein expression are associated with increased risk of SCCHN. AIM 3: To determine functional relevance of selected variant alleles and haplotypes of tSNPs of the 8 NER genes by correlating the frequencies of variant alleles/ haplotypes and genotypes/diplotypes with expression levels of mRNA and proteins of the 8 NER genes and DRC phenotype. This study will allow us to develop risk assessment models that integrate all biomarkers tested and epidemiological covariates. The relatively large sample size in this renewal allows for stratification analysis by tumor sites (i.e., oral cavity, pharynx and larynx), various genotypes/diplotypes and their combined genotypes, and epidemiologic covariates as well as for assessment of possible gene-gene and gene-environment interactions. This study will contribute to our understanding of the role of NER in the etiology of SCCHN and may lead to possible targets for primary prevention. PUBLIC HEALTH SIGNIFICANCE: This proposed study is to investigate the roles of genetic factors of DNA repair capacity (DRC), as well as their interactions with tobacco and alcohol use, in the etiology of squamous cell carcinomas of the oral cavity, pharynx, and larynx (SCCHN), expanding our preliminary findings to a role of DRC and its genetic determinants (85 single nucleotide polymorphisms, SNPs) in 8 DNA repair genes in a large study of 1600 cases and 1600 controls and applying our newly developed assays for mRNA and protein expression to 400 cases and 400 controls. Therefore, this study will help understand correlations between DRC genotypes (SNPs) and phenotypes (expression of mRNA and proteins and DRC) and their roles in the etiology of SCCHN. The long-term goal of this study is to identify effective biomarkers that can be used to identify at-risk individuals who will be targeted for primary prevention of SCCHN in the general population.